It is clear that the acquisition, maintenance, and dissemination of accessory elements have been central to the ongoing success of staphylococci as pathogens. Staphylococci represent a salient illustration of the adaptability afforded to microorganisms by access to additional functions through gene transfer mechanisms. Although DNA can be introduced into staphylococci in the laboratory via each of the three traditional bacterial gene transfer mechanisms—transformation, transduction, and conjugation—the latter two are believed to be the most significant mediators of natural genetic exchange. Most staphylococcal plasmids can be categorized as one of three main classes based on physical/genetic organization and functional characteristics, although another group, the pSK639 family plasmids, should be considered a fourth class. Staphylococcal insertion sequences and transposons are discussed in this chapter. Gene transfer mechanisms, together with accessory elements such as plasmids, transposable elements, prophages, and pathogenicity and resistance islands, serve as catalysts for microbial evolution by providing access to a shared reservoir of niche-adaptive functions. However, just as importantly, the combination of comparative genomics and sequence-based strain typing is clarifying the relationships between clinical Staphylococcus aureus strains. These studies are providing a new perspective on the scope and importance of the accessory genome, demonstrating that variation in pathogenic potential largely does not reside in the core genome, but rather that it is primarily attributable to the complement of mobile accessory elements that are present.

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